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- PDB-3o2r: Structural flexibility in region involved in dimer formation of n... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3o2r | ||||||
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Title | Structural flexibility in region involved in dimer formation of nuclease domain of Ribonuclase III (rnc) from Campylobacter jejuni | ||||||
![]() | (Ribonuclease III) x 2 | ||||||
![]() | HYDROLASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / nuclease domain / ribonuclase III | ||||||
Function / homology | ![]() ribonuclease III / ribonuclease III activity / tRNA processing / mRNA processing / rRNA processing / rRNA binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
![]() | ![]() Title: Structural Flexibility in Region Involved in Dimer Formation of Nuclease Domain of Ribonuclase III (rnc) from Campylobacter jejuni. Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.9 KB | Display | ![]() |
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PDB format | ![]() | 242.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 465.4 KB | Display | ![]() |
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Full document | ![]() | 471.5 KB | Display | |
Data in XML | ![]() | 35.3 KB | Display | |
Data in CIF | ![]() | 55.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3n3wS S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 19136.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 11168 / Gene: CJSA_1547, rnc / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: D3FPA5, UniProt: Q9PM40*PLUS, ribonuclease III #2: Protein | Mass: 19149.807 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: NCTC 11168 / Gene: CJSA_1547, rnc / Plasmid: pMCSG7 / Production host: ![]() ![]() References: UniProt: D3FPA5, UniProt: Q9PM40*PLUS, ribonuclease III #3: Chemical | ChemComp-CL / #4: Water | ChemComp-HOH / | Sequence details | IN CHAINS B AND D, RESIDUE 31 DISPLAYS MICROHETEROGENEITY AND APPEARS AS BOTH A METHYLATED LYSINE ...IN CHAINS B AND D, RESIDUE 31 DISPLAYS MICROHETER | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.83 Å3/Da / Density % sol: 32.6 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 4 Details: Protein solution: 7.6 mg/mL, 0.5M Sodium chloride, 0.01M Tris pH 8.3; Screen solution: PACT (B1), 0.1M MIB buffer pH 4.0, 25% w/v PEG1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 3, 2010 / Details: Beryllium lenses |
Radiation | Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→30 Å / Num. all: 151202 / Num. obs: 151202 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 11 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.25→1.27 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.359 / Mean I/σ(I) obs: 2.6 / Num. unique all: 7499 / % possible all: 99.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3N3W Resolution: 1.251→29.78 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 0.866 / SU ML: 0.018 / Isotropic thermal model: Isotropic Individually refined / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.409 Å2
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Refinement step | Cycle: LAST / Resolution: 1.251→29.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.251→1.283 Å / Total num. of bins used: 20
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